Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold451
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 596512
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 3 of 5
Found at i:231534 original size:12 final size:12
Alignment explanation
Indices: 231507--231550 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
231497 AAAATAAAAT
*
231507 ATTATATTTAATA
1 ATTATTTTTAA-A
231520 ATTATTTTTAAA
1 ATTATTTTTAAA
231532 ATTATTTTTTAAA
1 ATTA-TTTTTAAA
*
231545 AATATT
1 ATTATT
231551 AAAAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 7 0.25
13 21 0.75
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
ATTATTTTTAAA
Found at i:233008 original size:3 final size:3
Alignment explanation
Indices: 233000--233026 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
232990 CATGGTATGG
233000 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
233027 TGATATTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:233283 original size:19 final size:19
Alignment explanation
Indices: 233259--233297 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
233249 TATTTAAGTT
*
233259 TAAAAAT-TTATAGTTTAAA
1 TAAAAATATTA-AATTTAAA
233278 TAAAAATATTAAATTTAAA
1 TAAAAATATTAAATTTAAA
233297 T
1 T
233298 GAGAGGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
TAAAAATATTAAATTTAAA
Found at i:233405 original size:21 final size:19
Alignment explanation
Indices: 233381--233422 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
233371 TTGATTTGAT
233381 TTTTTTATTATTTAATATATA
1 TTTTTTA-TATTT-ATATATA
*
233402 TTTTTTATATTTATGTATA
1 TTTTTTATATTTATATATA
233421 TT
1 TT
233423 ATGTAATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 5 0.25
21 7 0.35
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTTTTATATTTATATATA
Found at i:233799 original size:2 final size:2
Alignment explanation
Indices: 233792--233847 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
233782 TTAAGCAAAG
233792 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
233834 TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA
233848 ATAATGTTGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:238065 original size:11 final size:11
Alignment explanation
Indices: 238030--238091 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
238020 ATTTCTGTCA
238030 AGAAAAAAA-G
1 AGAAAAAAAGG
*
238040 A-AAAAAAAGAA
1 AGAAAAAAAG-G
*
238051 AGAAAGAAAGG
1 AGAAAAAAAGG
238062 AGAAAAAAAGG
1 AGAAAAAAAGG
*
238073 A-AACAAAAA-A
1 AGAA-AAAAAGG
238083 AGAAAAAAA
1 AGAAAAAAA
238092 TTATATATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
9 7 0.17
10 9 0.21
11 19 0.45
12 7 0.17
ACGTcount: A:0.81, C:0.02, G:0.18, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAGG
Found at i:238070 original size:24 final size:21
Alignment explanation
Indices: 238033--238091 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 21
238023 TCTGTCAAGA
*
238033 AAAAAAGAAAAAAAAGAAAGA
1 AAAAAAGAAAAAAAAGAAACA
*
238054 AAGAAAGGAGAAAAAAAGGAAACA
1 AA-AAA--AGAAAAAAAAGAAACA
238078 AAAAAAGAAAAAAA
1 AAAAAAGAAAAAAA
238092 TTATATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 11 0.33
22 3 0.09
23 3 0.09
24 16 0.48
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (21 bp):
AAAAAAGAAAAAAAAGAAACA
Found at i:238889 original size:14 final size:14
Alignment explanation
Indices: 238870--238921 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
238860 TCAATTCGTG
238870 ATATTTTTATATAA
1 ATATTTTTATATAA
* *
238884 ATATTTATATATTA
1 ATATTTTTATATAA
238898 ATAATTCATTTTATATAA
1 AT-A-T--TTTTATATAA
238916 ATATTT
1 ATATTT
238922 ACATGTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
14 16 0.53
15 1 0.03
16 2 0.07
17 1 0.03
18 10 0.33
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATTTTTATATAA
Found at i:238910 original size:20 final size:22
Alignment explanation
Indices: 238887--238936 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 22
238877 TATATAAATA
238887 TTTATATATTAATAATT-CAT-
1 TTTATATATTAATAATTACATG
*
238907 TTTATATA--AATATTTACATG
1 TTTATATATTAATAATTACATG
238927 TTTATATATT
1 TTTATATATT
238937 TCTGTCATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.24
19 3 0.12
20 16 0.64
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTATATATTAATAATTACATG
Found at i:238912 original size:18 final size:19
Alignment explanation
Indices: 238886--238934 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
238876 TTATATAAAT
*
238886 ATTTATATATTAATAATT-C
1 ATTT-TATATAAATAATTAC
*
238905 ATTTTATATAAATATTTAC
1 ATTTTATATAAATAATTAC
238924 ATGTTTATATA
1 AT-TTTATATA
238935 TTTCTGTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 11 0.42
19 7 0.27
20 8 0.31
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (19 bp):
ATTTTATATAAATAATTAC
Found at i:239056 original size:15 final size:15
Alignment explanation
Indices: 239038--239132 Score: 55
Period size: 13 Copynumber: 6.7 Consensus size: 15
239028 TATATAAATT
239038 TTTTATATAATTAAA
1 TTTTATATAATTAAA
239053 TTTTA-ACT--TTAAA
1 TTTTATA-TAATTAAA
*
239066 TTTT-T-TTATTAAA
1 TTTTATATAATTAAA
*
239079 TATTT-TA-AAATAAA
1 T-TTTATATAATTAAA
239093 TTTTAT-TAATTATAA
1 TTTTATATAATTA-AA
* *
239108 TTTTATTTAATAAAAA
1 TTTTATATAAT-TAAA
239124 TTTT-TATAA
1 TTTTATATAA
239133 ATATTAAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 22
0.70 0.05 0.24
Matches are distributed among these distances:
11 1 0.02
13 18 0.28
14 16 0.25
15 18 0.28
16 10 0.16
17 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTTATATAATTAAA
Found at i:239110 original size:27 final size:27
Alignment explanation
Indices: 239038--239112 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 27
239028 TATATAAATT
**
239038 TTTTATATAATTAAATTTTAACTTTAAA
1 TTTTAT-TAATTAAATTTTAACAATAAA
*
239066 TTTT-TTTATTAAATATTTTAA-AATAAA
1 TTTTATTAATT-AA-ATTTTAACAATAAA
239093 TTTTATTAATTATAATTTTA
1 TTTTATTAATTA-AATTTTA
239113 TTTAATAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
26 4 0.10
27 18 0.46
28 17 0.44
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTTATTAATTAAATTTTAACAATAAA
Found at i:239562 original size:29 final size:30
Alignment explanation
Indices: 239521--239586 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
239511 AAATATTAAA
*
239521 TTTTTGATAAAAATTAAAT-TGATTTTATAT
1 TTTTTTATAAAAATTAAATATGA-TTTATAT
**
239551 TTTTTTAT-AAAATTTTATATGATTTATAT
1 TTTTTTATAAAAATTAAATATGATTTATAT
*
239580 TTATTTA
1 TTTTTTA
239587 ATCTGATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (30 bp):
TTTTTTATAAAAATTAAATATGATTTATAT
Found at i:247150 original size:32 final size:32
Alignment explanation
Indices: 247113--247227 Score: 117
Period size: 32 Copynumber: 3.7 Consensus size: 32
247103 ATTGACACGT
**
247113 TTTAATAACCATTAAATTTATAAGTAATTATG
1 TTTAATATTCATTAAATTTATAAGTAATTATG
* ** * *
247145 TTTAATATTTATTAAATTTACGAGTAATTTTA
1 TTTAATATTCATTAAATTTATAAGTAATTATG
* * *
247177 TTTGATATTCATTATATTTATAAATAATTATG
1 TTTAATATTCATTAAATTTATAAGTAATTATG
*
247209 TCT-A-ATTCATTAAATTTAT
1 TTTAATATTCATTAAATTTAT
247228 GATCAATATT
Statistics
Matches: 66, Mismatches: 17, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
30 14 0.21
31 1 0.02
32 51 0.77
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (32 bp):
TTTAATATTCATTAAATTTATAAGTAATTATG
Found at i:247905 original size:13 final size:12
Alignment explanation
Indices: 247887--247918 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
247877 CCAATTATAA
247887 AAAAAAAAAATAG
1 AAAAAAAAAA-AG
247900 AAAAAAAAAAAG
1 AAAAAAAAAAAG
247912 AAAAAAA
1 AAAAAAA
247919 GAGAGCCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.91, C:0.00, G:0.06, T:0.03
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:247905 original size:14 final size:13
Alignment explanation
Indices: 247885--247918 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
247875 GGCCAATTAT
*
247885 AAAAAAAAAAAAT
1 AAAAAAAAAAAAG
247898 AGAAAAAAAAAAAG
1 A-AAAAAAAAAAAG
247912 AAAAAAA
1 AAAAAAA
247919 GAGAGCCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.91, C:0.00, G:0.06, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:248307 original size:17 final size:17
Alignment explanation
Indices: 248285--248320 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
248275 TCATATCATA
248285 TATAAAATTATCAAGTT
1 TATAAAATTATCAAGTT
248302 TATAAAATTATCAAGTT
1 TATAAAATTATCAAGTT
248319 TA
1 TA
248321 CCCTCGCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (17 bp):
TATAAAATTATCAAGTT
Found at i:250982 original size:24 final size:24
Alignment explanation
Indices: 250948--251015 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
250938 TAAATATTTA
* *
250948 TTTAATCTTATATTTTAATATAATT
1 TTTAAT-TTATATTTTAAAAAAATT
250973 TTTAATTTAT-TATTTAAAAAAATT
1 TTTAATTTATAT-TTTAAAAAAATT
*
250997 ATTAATTTGATA-TTTAAAA
1 TTTAATTT-ATATTTTAAAA
251016 TTTTATTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
23 1 0.03
24 28 0.76
25 8 0.22
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (24 bp):
TTTAATTTATATTTTAAAAAAATT
Found at i:251342 original size:68 final size:68
Alignment explanation
Indices: 251258--251390 Score: 248
Period size: 68 Copynumber: 2.0 Consensus size: 68
251248 GACTAACGGC
251258 GTTAGTCTAAAAAGTAATATGCTTGATAAAATAAAAGTTTAAGTACTAAATTAATAATTTTTTCT
1 GTTAGTCTAAAAAGTAATATGCTTGATAAAATAAAAGTTTAAGTACTAAATTAATAATTTTTTCT
251323 GGT
66 GGT
* *
251326 GTTAGTCTAAAAAGTAATATGTTTGATAAAATAAAAGTTTAAGTATTAAATTAATAATTTTTTCT
1 GTTAGTCTAAAAAGTAATATGCTTGATAAAATAAAAGTTTAAGTACTAAATTAATAATTTTTTCT
251391 TCAGGTATCA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.41
Consensus pattern (68 bp):
GTTAGTCTAAAAAGTAATATGCTTGATAAAATAAAAGTTTAAGTACTAAATTAATAATTTTTTCT
GGT
Found at i:265793 original size:59 final size:59
Alignment explanation
Indices: 265630--266048 Score: 444
Period size: 59 Copynumber: 7.1 Consensus size: 59
265620 GGTCGCTTCA
* * ** * * * *
265630 TGGCTATCTGAGTTTGAGTGACTTGGCATCACTTGATATTTAAATTTGGGTCATCTTGG
1 TGGCGATCTGAATTTGAGTGACTTGGTGTCACTTGACATTTGAATTTGGGTCACCTCGG
* ** * ** * * *
265689 TGGCG-TCTAAATTTGAACGACTTGGCGTCACTTGATGTTTAAATTTGAGTCACCTCAG
1 TGGCGATCTGAATTTGAGTGACTTGGTGTCACTTGACATTTGAATTTGGGTCACCTCGG
* * **
265747 TGGCGATCTGAGTTTGAGTGACTCGGTGTCACTTGACATTTGAATTTGGGTTGCCTCGG
1 TGGCGATCTGAATTTGAGTGACTTGGTGTCACTTGACATTTGAATTTGGGTCACCTCGG
* * * ** *
265806 TGGCGATCTGAATTTGAGTGACTTGGTGTCACTTGACGTTTGAATTCGAGTTGCCTCAG
1 TGGCGATCTGAATTTGAGTGACTTGGTGTCACTTGACATTTGAATTTGGGTCACCTCGG
* ** * *
265865 TGGCAATCTGAATTTGAGTGACTTAATGTCACTCGACATTTGAATTTGGGTCACCTCAG
1 TGGCGATCTGAATTTGAGTGACTTGGTGTCACTTGACATTTGAATTTGGGTCACCTCGG
* * *
265924 TGGCGATCTGAATTTAAGTGACTTGGTGTCACTTGACGTTTGAATTTGGATCACCTCGG
1 TGGCGATCTGAATTTGAGTGACTTGGTGTCACTTGACATTTGAATTTGGGTCACCTCGG
* * * * * * **
265983 TGGTGATCTAAATTTAAGTGACTTAGTGTCACTTAACATTTGAGTTTGGGTCGTCTCGG
1 TGGCGATCTGAATTTGAGTGACTTGGTGTCACTTGACATTTGAATTTGGGTCACCTCGG
266042 TGGCGAT
1 TGGCGAT
266049 TGGGGCATAT
Statistics
Matches: 302, Mismatches: 57, Indels: 2
0.84 0.16 0.01
Matches are distributed among these distances:
58 48 0.16
59 254 0.84
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.36
Consensus pattern (59 bp):
TGGCGATCTGAATTTGAGTGACTTGGTGTCACTTGACATTTGAATTTGGGTCACCTCGG
Found at i:265881 original size:118 final size:118
Alignment explanation
Indices: 265630--266048 Score: 491
Period size: 118 Copynumber: 3.6 Consensus size: 118
265620 GGTCGCTTCA
* * * ** * * * *
265630 TGGCTATCTGAGTTTGAGTGACTTGGCATCACTTGATATTTAAATTTGGGTCATCTTGGTGGCG-
1 TGGCGATCTGAATTTGAGTGACTTAGTGTCACTTGACATTTGAATTTGGGTCACCTCGGTGGCGA
* ** * * *
265694 TCTAAATTTGAACGACTTGGCGTCACTTGATGTTTAAATTTGAGTCACCTCAG
66 TCTGAATTTGAGTGACTTGGTGTCACTTGACGTTTGAATTTGAGTCACCTCAG
* ** **
265747 TGGCGATCTGAGTTTGAGTGACTCGGTGTCACTTGACATTTGAATTTGGGTTGCCTCGGTGGCGA
1 TGGCGATCTGAATTTGAGTGACTTAGTGTCACTTGACATTTGAATTTGGGTCACCTCGGTGGCGA
* **
265812 TCTGAATTTGAGTGACTTGGTGTCACTTGACGTTTGAATTCGAGTTGCCTCAG
66 TCTGAATTTGAGTGACTTGGTGTCACTTGACGTTTGAATTTGAGTCACCTCAG
* * * *
265865 TGGCAATCTGAATTTGAGTGACTTAATGTCACTCGACATTTGAATTTGGGTCACCTCAGTGGCGA
1 TGGCGATCTGAATTTGAGTGACTTAGTGTCACTTGACATTTGAATTTGGGTCACCTCGGTGGCGA
* *
265930 TCTGAATTTAAGTGACTTGGTGTCACTTGACGTTTGAATTTG-GATCACCTCGG
66 TCTGAATTTGAGTGACTTGGTGTCACTTGACGTTTGAATTTGAG-TCACCTCAG
* * * * * **
265983 TGGTGATCTAAATTTAAGTGACTTAGTGTCACTTAACATTTGAGTTTGGGTCGTCTCGGTGGCGA
1 TGGCGATCTGAATTTGAGTGACTTAGTGTCACTTGACATTTGAATTTGGGTCACCTCGGTGGCGA
266048 T
66 T
266049 TGGGGCATAT
Statistics
Matches: 256, Mismatches: 44, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
117 55 0.21
118 201 0.79
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.36
Consensus pattern (118 bp):
TGGCGATCTGAATTTGAGTGACTTAGTGTCACTTGACATTTGAATTTGGGTCACCTCGGTGGCGA
TCTGAATTTGAGTGACTTGGTGTCACTTGACGTTTGAATTTGAGTCACCTCAG
Found at i:270756 original size:13 final size:13
Alignment explanation
Indices: 270738--270768 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
270728 CCATTAACTA
270738 ATCTTATTCTTGG
1 ATCTTATTCTTGG
270751 ATCTTATTCTTGG
1 ATCTTATTCTTGG
270764 ATCTT
1 ATCTT
270769 GTTCGTGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.16, G:0.13, T:0.55
Consensus pattern (13 bp):
ATCTTATTCTTGG
Found at i:276560 original size:15 final size:15
Alignment explanation
Indices: 276540--276573 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
276530 AAGTTATAAG
*
276540 AAAAAAATAATAATA
1 AAAAAAATAAAAATA
276555 AAAAAAATAAAAATA
1 AAAAAAATAAAAATA
276570 AAAA
1 AAAA
276574 CTTTGGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAAAAATAAAAATA
Found at i:277216 original size:16 final size:15
Alignment explanation
Indices: 277195--277225 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
277185 TAAAATTAAA
277195 AAAATAATAACAAAAT
1 AAAATAATAA-AAAAT
277211 AAAATAATAAAAAAT
1 AAAATAATAAAAAAT
277226 TCTTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAATAATAAAAAAT
Found at i:289943 original size:42 final size:42
Alignment explanation
Indices: 289890--291193 Score: 1205
Period size: 42 Copynumber: 31.0 Consensus size: 42
289880 TTCATTTTTT
* *
289890 TCCCTTAGTCTGCCTATCGACTTTGACCCTGGAGACTTTTCA
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * * *
289932 TCCCTTAGTCTGCCTATCGG-TTTCATCCCTGGAGACTTTCCT
1 TCCCTTAGTCTGCCTGTCGGCTTTGA-CCCTGGAGACTTTTCA
* * * * * *
289974 TCTCTCAGTCTGCCTGTCGGCTTTGACCTTGAAGACTTTCCT
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * * *
290016 TCCCTCAGTCTGCCAGTCGGCTTTGACCCTGAAAACTTTTCA
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * * * * *
290058 ACCCTCAGTCTGCCTATCGG-TTTAACCCTGGAGACTTTCCT
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * * *
290099 TCCCTTAGTCTACCTGTCGGCTTCGTCCCTAGAGACTTTTC-
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* *
290140 TACCCTCAGTCTGCATGTCGGCTTTGACCCTGGAGACTTTTCA
1 T-CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * *
290183 ACCCTTAGTCTGTCTGTCGGCTTTGACTCTGGAGAC-TTTCA
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * * * *
290224 ACCCTCAATCTGCCTATCGACTTTGACCCTGGAGACTTTTCA
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
*
290266 TCCCTTAGTCTGCTTGTCGGCTTTGACCCTGGAGACTTTTC-
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * * *
290307 TACCCTCAGTCTGCCTGCCGACTTTGACCTTGGAGACTTTTCA
1 T-CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * * **
290350 TCCCTCAGTTTGCCTGTCGCCTTTGACCCTAAAGACTTTTCA
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * *
290392 ACCCTTAGTCTACCTGTCGGCTTTAACCCTGGAGACTTTTCA
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* *
290434 TCCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTTCA
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * *
290476 ACCCTCAGTCTGCTTGTCGACAGCTTTGACCCTGGAGACTTTTCA
1 TCCCTTAGTCTGCCTGTCG---GCTTTGACCCTGGAGACTTTTCA
* *
290521 ACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * * * * *
290563 ACCCTCAGTCTGCCTATCGGCTTTGACCTTTGAGACTTTTTA
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * * * * *
290605 ACCCTCAGTCTGCTTGTCGGCTTTGACCCTAGAGACTTTCCT
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * * * * *
290647 TCCCTTAGTTTGCTTGTCGGCCTTGATCTTGGAGAC-TTTCC
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * *
290688 TACCTTTCAGTCTGTCTGTCGGCTTTGACCCTGGAGAC-TTTCC
1 T-CCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * * * **
290731 TACCCTTCAGTTTGCCTGTCGGCTTCGTCCCTAGAGACTGCCTCA
1 T-CCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACT-TTTCA
* * *
290776 T--CTAAAGTCTGCCTATCGGTTTTGACCCTGGAGACTTTTCA
1 TCCCT-TAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * ** *
290817 TCCCTTAGTCTGCTTATCGATTTTGACCCTGAAGACTTTTC-
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * * **
290858 TACCCTTCAGTCTGCCTGTCGGC-TTCATTCATGGAGACTGCCTCA
1 T-CCCTT-AGTCTGCCTGTCGGCTTTGA-CCCTGGAGACT-TTTCA
* * *
290903 T--CTAAAGTCTACCTGTCAGCTTTGACCCTGGAGACTTTTCA
1 TCCCT-TAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * ** * * *
290944 TCCCTTAGTTTACCTGTCGTTTTTTACCCTAGAGACTTTTCT
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * *
290986 TCCCTTAGTCTGTCTGTCGGCTTTGACTCTGGAGACTTTTTA
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * * *
291028 ACCCTTAGTCTGCCCGTCAGCTTTGACTCTGGAGACTTTTCA
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * * * * * *
291070 TCCCTTAGTTTGCCAGTC-GATTTAACCTTGGAGACTTTCCT
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * * * *
291111 TCCCTCAGTCTGCCTGTCGGCTTTGACCTTAGAGACTTTCCT
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * *
291153 TCCCTCAGTCTGCCTGTTGGCTTTGTCCCTGGAGACTTTTC
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
291194 TTTCTCTAAG
Statistics
Matches: 1040, Mismatches: 194, Indels: 56
0.81 0.15 0.04
Matches are distributed among these distances:
41 118 0.11
42 784 0.75
43 92 0.09
44 2 0.00
45 44 0.04
ACGTcount: A:0.15, C:0.31, G:0.19, T:0.36
Consensus pattern (42 bp):
TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
Found at i:291734 original size:17 final size:17
Alignment explanation
Indices: 291708--291741 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
291698 TATCCAATAT
*
291708 AATAATAAAAATCAAGA
1 AATAAAAAAAATCAAGA
*
291725 AATAAAAAAATTCAAGA
1 AATAAAAAAAATCAAGA
291742 TAAATCAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (17 bp):
AATAAAAAAAATCAAGA
Found at i:292883 original size:14 final size:14
Alignment explanation
Indices: 292864--292892 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
292854 ATTAGAAGTT
292864 ATAAGAAAAAAATA
1 ATAAGAAAAAAATA
292878 ATAAGAAAAAAATA
1 ATAAGAAAAAAATA
292892 A
1 A
292893 AAATAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
ATAAGAAAAAAATA
Found at i:292900 original size:14 final size:14
Alignment explanation
Indices: 292866--292901 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
292856 TAGAAGTTAT
*
292866 AAGAAAAAAATAAT
1 AAGAAAAAAATAAA
292880 AAGAAAAAAATAAA
1 AAGAAAAAAATAAA
*
292894 AATAAAAA
1 AAGAAAAA
292902 CTTTGGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (14 bp):
AAGAAAAAAATAAA
Found at i:296448 original size:13 final size:14
Alignment explanation
Indices: 296398--296448 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
296388 AAAATTTTAT
296398 AAATATATTTATATAA
1 AAATATATTTA-AT-A
296414 ATAATACATATTTAATA
1 A-AAT--ATATTTAATA
296431 AAATATATTTAA-A
1 AAATATATTTAATA
296444 AAATA
1 AAATA
296449 AATAATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
13 6 0.19
14 8 0.25
16 4 0.12
17 5 0.16
18 2 0.06
19 7 0.22
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATATATTTAATA
Found at i:296494 original size:13 final size:12
Alignment explanation
Indices: 296475--296505 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
296465 AATATAAATA
296475 TTTTATAAATTT
1 TTTTATAAATTT
296487 TATTTATAAATTT
1 T-TTTATAAATTT
296500 TTTTAT
1 TTTTAT
296506 CTATCTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTATAAATTT
Found at i:297170 original size:2 final size:2
Alignment explanation
Indices: 297163--297192 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
297153 GGCGAAGGAA
297163 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
297193 CTGAAACGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:302394 original size:2 final size:2
Alignment explanation
Indices: 302389--302413 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
302379 ACTTACAATT
302389 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
302414 TACTTTAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:304067 original size:138 final size:137
Alignment explanation
Indices: 303879--304147 Score: 394
Period size: 138 Copynumber: 2.0 Consensus size: 137
303869 TAAGAATTTT
* *
303879 TCATTGATGATGAAGATTTAAAATTGTCAAACAAATGTAGCAATCAGAAATTCATATTTGACGTT
1 TCATTGATGATAAAGATTTAAAATTGTCAAACAAATGTAGCAATCAGAAATCCATATTTGACGTT
* * *
303944 GTTTGTAAGGTATCTCTTGGAGATTATAACCATACAATGTTGCTAGCATGAGTTCCTACATATTT
66 GTTTATAAGATATCTCTGGGAGATTATAACCATACAATGTTGCTAGCATGAGTTCCTACATATTT
304009 TAAGTGC
131 TAAGTGC
* * * * * *
304016 TCATTGGATGATAAAGCTTTAAAATTGTCGAACAAATGTAGTAATTAGAAATCCGTATTTGACTT
1 TCATT-GATGATAAAGATTTAAAATTGTCAAACAAATGTAGCAATCAGAAATCCATATTTGACGT
* * * *
304081 TGTTTATAAGATATCTCTGGGAGATTATAACTATATAATGTTGCTTGCTTGAGTTCCTACATATT
65 TGTTTATAAGATATCTCTGGGAGATTATAACCATACAATGTTGCTAGCATGAGTTCCTACATATT
304146 TT
130 TT
304148 GAATGTTCTT
Statistics
Matches: 116, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
137 5 0.04
138 111 0.96
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (137 bp):
TCATTGATGATAAAGATTTAAAATTGTCAAACAAATGTAGCAATCAGAAATCCATATTTGACGTT
GTTTATAAGATATCTCTGGGAGATTATAACCATACAATGTTGCTAGCATGAGTTCCTACATATTT
TAAGTGC
Found at i:306471 original size:24 final size:24
Alignment explanation
Indices: 306444--306493 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
306434 TTTCTTAATT
306444 AATTGA-TTA-TATAATTAATAATAA
1 AATTGATTTATTAT-ATTAA-AATAA
*
306468 AATTTATTTATTATATTAAAATAA
1 AATTGATTTATTATATTAAAATAA
306492 AA
1 AA
306494 ATTTGTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 12 0.52
25 8 0.35
26 3 0.13
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
AATTGATTTATTATATTAAAATAA
Found at i:309156 original size:13 final size:13
Alignment explanation
Indices: 309138--309163 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
309128 TAATAATCTA
309138 GCAAATCCCACAT
1 GCAAATCCCACAT
309151 GCAAATCCCACAT
1 GCAAATCCCACAT
309164 CTTCAAGCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.38, G:0.08, T:0.15
Consensus pattern (13 bp):
GCAAATCCCACAT
Found at i:310075 original size:54 final size:54
Alignment explanation
Indices: 309909--310081 Score: 143
Period size: 54 Copynumber: 3.2 Consensus size: 54
309899 CCCATACTCT
* * * * * *
309909 GGTCTTCC-GCCATACCCAGATCCGAATTCAGGCGGTGGAGGCCGCTCAAATTCG
1 GGTC-TCCGGCCATACCCAGATCCGAACTCCGGAGGAGGCGGCTGCTCAAATTCG
* * * ** * ** *
309963 GGTCTCCGCCCATACCCGGATCCGAAGTCCGGTTGA-TCTGGCTGCTCGTATGCG
1 GGTCTCCGGCCATACCCAGATCCGAACTCCGGAGGAGGC-GGCTGCTCAAATTCG
* * *
310017 GGTCTCTGGCCATACCCAGATCCAAACTCCGGAGGAGGCGGCTGCTCAAATTCA
1 GGTCTCCGGCCATACCCAGATCCGAACTCCGGAGGAGGCGGCTGCTCAAATTCG
*
310071 GGTCTTCGGCC
1 GGTCTCCGGCC
310082 GTAATCAGTT
Statistics
Matches: 89, Mismatches: 27, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
53 3 0.03
54 85 0.96
55 1 0.01
ACGTcount: A:0.18, C:0.32, G:0.28, T:0.21
Consensus pattern (54 bp):
GGTCTCCGGCCATACCCAGATCCGAACTCCGGAGGAGGCGGCTGCTCAAATTCG
Found at i:310688 original size:11 final size:11
Alignment explanation
Indices: 310672--310706 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
310662 TAATTATTTT
310672 AAAATATTTAA
1 AAAATATTTAA
310683 AAAATATTTAA
1 AAAATATTTAA
310694 AATAATATATTAA
1 AA-AATAT-TTAA
310707 TATATTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.59
12 5 0.23
13 4 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AAAATATTTAA
Found at i:310718 original size:28 final size:27
Alignment explanation
Indices: 310685--310737 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
310675 ATATTTAAAA
310685 AATA-TTTAAAATAATATATTAATATATT
1 AATATTTTAAAAT-ATATA-TAATATATT
*
310713 AATATTTTAAAATTTATATAATATA
1 AATATTTTAAAATATATATAATATA
310738 AATTATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 7 0.30
28 8 0.35
29 8 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
AATATTTTAAAATATATATAATATATT
Found at i:312688 original size:17 final size:18
Alignment explanation
Indices: 312654--312690 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
312644 TTCTCATGTG
312654 TTTTAAGTTTTGTATTTT
1 TTTTAAGTTTTGTATTTT
312672 TTTTAAGTTTTGT-TTTT
1 TTTTAAGTTTTGTATTTT
312689 TT
1 TT
312691 AGTTTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.76
Consensus pattern (18 bp):
TTTTAAGTTTTGTATTTT
Found at i:313292 original size:21 final size:21
Alignment explanation
Indices: 313268--313308 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
313258 ATTTTAGATT
313268 TTGAA-AATTTTTAAATATTTA
1 TTGAATAA-TTTTAAATATTTA
*
313289 TTGAATAATTTTAGATATTT
1 TTGAATAATTTTAAATATTT
313309 TAATAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (21 bp):
TTGAATAATTTTAAATATTTA
Found at i:313316 original size:21 final size:21
Alignment explanation
Indices: 313255--313317 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
313245 TTTTTTTTAC
*
313255 ATAATTTTAGAT-TTTGAA-A
1 ATAATTTTAGATATTTTAATA
* *
313274 AT--TTTTAAATA-TTTATTGA
1 ATAATTTTAGATATTTTAAT-A
313293 ATAATTTTAGATATTTTAATA
1 ATAATTTTAGATATTTTAATA
313314 ATAA
1 ATAA
313318 AATGTATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
17 10 0.30
19 5 0.15
21 13 0.39
22 5 0.15
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (21 bp):
ATAATTTTAGATATTTTAATA
Found at i:313601 original size:155 final size:157
Alignment explanation
Indices: 313422--313716 Score: 495
Period size: 155 Copynumber: 1.9 Consensus size: 157
313412 ATAAAATTTG
* * *
313422 TTTTCTATAATTTTAGATTTTAATATTTTTAAAATATTTATCTAATAAATTTAAATATTTTAATA
1 TTTTCTATAATTTTAGAATTTAATATTTTAAAAATATTTACCTAATAAATTTAAATATTTTAATA
* *
313487 ACAAAAATATATAAAAAGTAAATTAATTAACTGAAAAAAAACTATAGAAAAAACAAAACTGAAAA
66 ACAAAAATATATAAAAAATAAATTAATTAACTGAAAAAAAACTATAGAAAAAACAAAACTAAAAA
*
313552 AAAATAAAAATCCAATAATTTATTGAA
131 AAAAAAAAAATCCAATAATTTATTGAA
*
313579 TTTT-TATAATTTTA-AATTTAATATTTTAAAAATATTTACCTGATAAATTTAAATATTTTAATA
1 TTTTCTATAATTTTAGAATTTAATATTTTAAAAATATTTACCTAATAAATTTAAATATTTTAATA
* *
313642 ATAAAAATATATAAAAAATAAATTAATTAACTGAAAAAAAACTATAGAAAAAACAAAATTAAAAA
66 ACAAAAATATATAAAAAATAAATTAATTAACTGAAAAAAAACTATAGAAAAAACAAAACTAAAAA
313707 AAAAAAAAAA
131 AAAAAAAAAA
313717 AACTTAAAAA
Statistics
Matches: 129, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
155 115 0.89
156 10 0.08
157 4 0.03
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (157 bp):
TTTTCTATAATTTTAGAATTTAATATTTTAAAAATATTTACCTAATAAATTTAAATATTTTAATA
ACAAAAATATATAAAAAATAAATTAATTAACTGAAAAAAAACTATAGAAAAAACAAAACTAAAAA
AAAAAAAAAATCCAATAATTTATTGAA
Found at i:313712 original size:20 final size:20
Alignment explanation
Indices: 313689--313726 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
313679 AAAACTATAG
*
313689 AAAAAACAAAA-TTAAAAAA
1 AAAAAAAAAAACTTAAAAAA
313708 AAAAAAAAAAACTTAAAAA
1 AAAAAAAAAAACTTAAAAA
313727 GCATGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.84, C:0.05, G:0.00, T:0.11
Consensus pattern (20 bp):
AAAAAAAAAAACTTAAAAAA
Found at i:321166 original size:21 final size:21
Alignment explanation
Indices: 321142--321184 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
321132 AAAACCTAGA
321142 TTGTTTCCTTCTTTTAACATG
1 TTGTTTCCTTCTTTTAACATG
321163 TTGTTTCCTTCTTTTAACATG
1 TTGTTTCCTTCTTTTAACATG
321184 T
1 T
321185 CTCACATGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.19, G:0.09, T:0.58
Consensus pattern (21 bp):
TTGTTTCCTTCTTTTAACATG
Found at i:321637 original size:2 final size:2
Alignment explanation
Indices: 321630--321661 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
321620 GCTTATTTCC
321630 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
321662 GTGTGGGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:321666 original size:2 final size:2
Alignment explanation
Indices: 321661--321698 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
321651 TATATATATA
* *
321661 TG TG TG GG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
321699 GTTTTTAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.03, C:0.00, G:0.50, T:0.47
Consensus pattern (2 bp):
TG
Found at i:324924 original size:16 final size:16
Alignment explanation
Indices: 324899--324954 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
324889 ACAATAACAT
*
324899 TTATATATTTTATATA
1 TTATAAATTTTATATA
324915 TTATAAATTTTATAT-
1 TTATAAATTTTATATA
*
324930 TTATATAATTTTTTA-A
1 TTATA-AATTTTATATA
*
324946 ATATAAATT
1 TTATAAATT
324955 GTGGGTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 9 0.26
16 26 0.74
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATAAATTTTATATA
Found at i:328907 original size:19 final size:19
Alignment explanation
Indices: 328869--328907 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
328859 ATAATCAATT
*
328869 TATTCGATCAAATTGATTA
1 TATTCGATCAAATCGATTA
* *
328888 TATTCGATCCAATCGGTTA
1 TATTCGATCAAATCGATTA
328907 T
1 T
328908 GAAATTATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (19 bp):
TATTCGATCAAATCGATTA
Found at i:331286 original size:18 final size:18
Alignment explanation
Indices: 331228--331296 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
331218 CCAACATAAC
*
331228 ATAAATATTAAAATTTAT
1 ATAATTATTAAAATTTAT
*
331246 ATAA-TA-CAAAA-TTAT
1 ATAATTATTAAAATTTAT
331261 -TAAGTTATTAAAATTTAT
1 ATAA-TTATTAAAATTTAT
331279 ATAATTATTAAAAATTTA
1 ATAATTATT-AAAATTTA
331297 AGCATAATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
14 3 0.07
15 4 0.09
16 6 0.14
17 6 0.14
18 13 0.30
19 11 0.26
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (18 bp):
ATAATTATTAAAATTTAT
Found at i:334041 original size:328 final size:331
Alignment explanation
Indices: 333433--334087 Score: 1091
Period size: 328 Copynumber: 2.0 Consensus size: 331
333423 TGTGAATTAT
* *
333433 TTTTCTTTGCTGATTCAAAAATTCACATGAAACATGCAACTAATACATCCATTCAAAGATTCTAA
1 TTTTCTTTGCTGAATCAAAAATTCACATGAAACATGCAACTAATACATCCATTCAAAGATTCCAA
** * *
333498 GTATGGTACAAAATCGAAGTCCCCTTAAAGCTATGTCAAAGCACATCAAAATATGACATAAATAT
66 GTACAGTACAAAATC--A--CCCCTTAAAGCTATGTCAAAGCACATAAAAATATGACACAAATAT
*
333563 TGCAGTTCAACAACTGCAAACTAGCTCCAATCACAACATACATCCTACTTTATACTTCAGAATTA
127 TGCAGTTCAACAACTGCAAACTAACTCCAATCACAACATACATCCTACTTTATACTTCAGAATTA
333628 CATTCTAAATTCCCAGTTTATCACCTAAAATTCAGGCATTTCAAACTCTTTGCTTAGATATACTT
192 CATTCTAAATTCCCAGTTTATCACCTAAAATTCAGGCATTTCAAACTCTTTGCTTAGATATACTT
* *
333693 AAGTTAAAGTTCCAAAATCAAAGTCGTAACTAAAGGTTTAATTCTTTTTCCCTAATCTACATCAA
257 AACTTAAAGTTCCAAAATCAAAGTCGTAACTAAAGGTTTAATTCTTTTCCCCTAATCTACATCAA
333758 TGCCTTAAAA
322 TGCCTTAAAA
333768 TTTTCTTTGCTGAATCAAAAATTCACATGAAACATGCAACTAATACATCCATTCAAAGATTCCAA
1 TTTTCTTTGCTGAATCAAAAATTCACATGAAACATGCAACTAATACATCCATTCAAAGATTCCAA
*
333833 GTACAGTAC-AAA-C-CCTCTTAAAGCTATGTCAAAGCACATAAAAATATGACACAAATATTGCA
66 GTACAGTACAAAATCACCCCTTAAAGCTATGTCAAAGCACATAAAAATATGACACAAATATTGCA
* *
333895 TTTCAACAACTGCAAACTAATTCCAATCACAACATACATCCTACTTTATACTTCAGAATTACATT
131 GTTCAACAACTGCAAACTAACTCCAATCACAACATACATCCTACTTTATACTTCAGAATTACATT
* * *
333960 CTAAATTCCCAGTTTATCGCCTAAAATTCAGGCATTTCAACCTCTTTGCTTAGATATATTTAACT
196 CTAAATTCCCAGTTTATCACCTAAAATTCAGGCATTTCAAACTCTTTGCTTAGATATACTTAACT
* * *
334025 TAAAGTTCCGAAATCAAAGTGGTAACTAAAGGTTTAATTCTTTTCCCCTAATCTACATTAATG
261 TAAAGTTCCAAAATCAAAGTCGTAACTAAAGGTTTAATTCTTTTCCCCTAATCTACATCAATG
334088 GCTGACAAAT
Statistics
Matches: 302, Mismatches: 18, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
328 228 0.75
333 1 0.00
334 3 0.01
335 70 0.23
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.32
Consensus pattern (331 bp):
TTTTCTTTGCTGAATCAAAAATTCACATGAAACATGCAACTAATACATCCATTCAAAGATTCCAA
GTACAGTACAAAATCACCCCTTAAAGCTATGTCAAAGCACATAAAAATATGACACAAATATTGCA
GTTCAACAACTGCAAACTAACTCCAATCACAACATACATCCTACTTTATACTTCAGAATTACATT
CTAAATTCCCAGTTTATCACCTAAAATTCAGGCATTTCAAACTCTTTGCTTAGATATACTTAACT
TAAAGTTCCAAAATCAAAGTCGTAACTAAAGGTTTAATTCTTTTCCCCTAATCTACATCAATGCC
TTAAAA
Found at i:338321 original size:2 final size:2
Alignment explanation
Indices: 338316--338343 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
338306 GTGTTAATAC
338316 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
338344 TAATATAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:338653 original size:15 final size:15
Alignment explanation
Indices: 338625--338655 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
338615 TATTATATAT
*
338625 ATATATATATATTTA
1 ATATAAATATATTTA
338640 ATATAAATATATTTA
1 ATATAAATATATTTA
338655 A
1 A
338656 CTTTTTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATAAATATATTTA
Found at i:339047 original size:29 final size:30
Alignment explanation
Indices: 339014--339071 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
339004 TTTAAAATTT
* *
339014 AATTTTATTGATTT-ATATATAATTTTTAA
1 AATTTGATTGATTTAATATATAATATTTAA
*
339043 AATTTGATTTATTTAATATATAATATTTA
1 AATTTGATTGATTTAATATATAATATTTA
339072 TATTAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (30 bp):
AATTTGATTGATTTAATATATAATATTTAA
Found at i:339070 original size:23 final size:25
Alignment explanation
Indices: 339021--339070 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 25
339011 TTTAATTTTA
* *
339021 TTGATTTATATATAATTTTTAAAAT
1 TTGATTTATATATAATATATAAAAT
*
339046 TTGATTTAT-T-TAATATATAATAT
1 TTGATTTATATATAATATATAAAAT
339069 TT
1 TT
339071 ATATTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 12 0.55
24 1 0.05
25 9 0.41
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (25 bp):
TTGATTTATATATAATATATAAAAT
Found at i:339559 original size:4 final size:4
Alignment explanation
Indices: 339552--339580 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
339542 ATATATATAT
339552 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
339581 CCAACATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:340516 original size:21 final size:22
Alignment explanation
Indices: 340490--340541 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
340480 ATAATAATTG
*
340490 ATAAAATTAAT-TATTATTATA
1 ATAAAATTAATATATTATAATA
*
340511 ATAAAATT-ATATATTATAATG
1 ATAAAATTAATATATTATAATA
*
340532 ATAAGATTAA
1 ATAAAATTAA
340542 AATTTATGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 2 0.08
21 23 0.88
22 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
ATAAAATTAATATATTATAATA
Found at i:340916 original size:23 final size:24
Alignment explanation
Indices: 340888--340933 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
340878 TACTTGATTA
*
340888 TATAATTAA-TAAAATTTATTTAT
1 TATAATTAATTAAAAATTATTTAT
340911 TATAATTAATTAAAAATTATTTA
1 TATAATTAATTAAAAATTATTTA
340934 CATTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TATAATTAATTAAAAATTATTTAT
Found at i:342879 original size:26 final size:26
Alignment explanation
Indices: 342841--342923 Score: 68
Period size: 25 Copynumber: 3.2 Consensus size: 26
342831 AATCAAATTT
342841 TTTAAAT-TCAAATAAAAATTTATAAA
1 TTTAAATAT-AAATAAAAATTTATAAA
*
342867 TTTAAATATAAATATAAAA--TATAAT
1 TTTAAATATAAATA-AAAATTTATAAA
* *
342892 TTTCAAA-ACATATAAAAATTT-TAAA
1 TTT-AAATATAAATAAAAATTTATAAA
342917 TATTAAA
1 T-TTAAA
342924 CATCCACTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
24 4 0.09
25 20 0.43
26 18 0.38
27 5 0.11
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.39
Consensus pattern (26 bp):
TTTAAATATAAATAAAAATTTATAAA
Found at i:347689 original size:18 final size:16
Alignment explanation
Indices: 347647--347689 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
347637 TTTAATAAAG
*
347647 ATTTTAATAGAAATAA
1 ATTTTAATAAAAATAA
*
347663 ATATTAATACAAAATAA
1 ATTTTAATA-AAAATAA
347680 TATTTTAATA
1 -ATTTTAATA
347690 TTGTTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 8 0.36
17 6 0.27
18 8 0.36
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
ATTTTAATAAAAATAA
Found at i:349287 original size:62 final size:63
Alignment explanation
Indices: 349212--349338 Score: 238
Period size: 62 Copynumber: 2.0 Consensus size: 63
349202 AAAAAAAAAA
*
349212 AAATAGAATTCCAACTCTATATGAAAGTCAGCAAATAAA-TTAAAAAAAAAACAATTAATGTC
1 AAATAAAATTCCAACTCTATATGAAAGTCAGCAAATAAATTTAAAAAAAAAACAATTAATGTC
349274 AAATAAAATTCCAACTCTATATGAAAGTCAGCAAATAAATTTAAAAAAAAAACAATTAATGTC
1 AAATAAAATTCCAACTCTATATGAAAGTCAGCAAATAAATTTAAAAAAAAAACAATTAATGTC
349337 AA
1 AA
349339 TCAACTAAGT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
62 38 0.60
63 25 0.40
ACGTcount: A:0.56, C:0.13, G:0.07, T:0.24
Consensus pattern (63 bp):
AAATAAAATTCCAACTCTATATGAAAGTCAGCAAATAAATTTAAAAAAAAAACAATTAATGTC
Found at i:353992 original size:12 final size:12
Alignment explanation
Indices: 353977--354021 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
353967 ATAATTACGT
353977 AAATAAAATAAA
1 AAATAAAATAAA
353989 AAATAAAATAAA
1 AAATAAAATAAA
*
354001 AATTGAAATATAATA
1 AAAT-AAA-ATAA-A
354016 AAATAA
1 AAATAA
354022 TTTTGCTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 15 0.54
13 3 0.11
14 6 0.21
15 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (12 bp):
AAATAAAATAAA
Found at i:354429 original size:34 final size:32
Alignment explanation
Indices: 354391--354476 Score: 82
Period size: 40 Copynumber: 2.4 Consensus size: 32
354381 TAGTTTAAAA
354391 TATAAATATTTTTTTGTTTAAATTTATTTATATT
1 TATAAATATTTTTTTG-TTAAATTTATTTATA-T
354425 TATAAATGAATAATTTAACTTTGTTAAATTTATTTATAT
1 TATAAAT--AT--TTT---TTTGTTAAATTTATTTATAT
*
354464 TATATATATTTTT
1 TATAAATATTTTT
354477 AAAATATTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 16
0.72 0.02 0.26
Matches are distributed among these distances:
32 1 0.02
34 7 0.16
35 3 0.07
36 2 0.05
37 2 0.05
38 3 0.07
39 7 0.16
40 15 0.34
41 4 0.09
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.59
Consensus pattern (32 bp):
TATAAATATTTTTTTGTTAAATTTATTTATAT
Found at i:355032 original size:16 final size:17
Alignment explanation
Indices: 355011--355042 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
355001 TAAATTTAAA
355011 TAAATAA-TTTAATTTT
1 TAAATAATTTTAATTTT
355027 TAAATAATTTTAATTT
1 TAAATAATTTTAATTT
355043 ATACAAATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAATAATTTTAATTTT
Found at i:358076 original size:32 final size:32
Alignment explanation
Indices: 358040--358118 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 32
358030 CTATAATTTT
**
358040 TTTAATATTATTATTACAT-TTTAATTAATTGA
1 TTTAATATTATTATT-CATGGCTAATTAATTGA
* *
358072 TTTAAATATTGTT-TTCATGGCTAATTAATTGC
1 TTT-AATATTATTATTCATGGCTAATTAATTGA
*
358104 TTTAATTTTATTATT
1 TTTAATATTATTATT
358119 TGTTAATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
31 10 0.26
32 20 0.53
33 8 0.21
ACGTcount: A:0.32, C:0.05, G:0.06, T:0.57
Consensus pattern (32 bp):
TTTAATATTATTATTCATGGCTAATTAATTGA
Found at i:358131 original size:80 final size:80
Alignment explanation
Indices: 358041--358200 Score: 295
Period size: 80 Copynumber: 2.0 Consensus size: 80
358031 TATAATTTTT
358041 TTAATATTATTATTACATTTTAATTAATTGATTTAAATATTGTTT-TCATGGCTAATTAATTGCT
1 TTAATATTATTATTACATTTTAATTAATTGATTTAAATATTGTTTCT-ATGGCTAATTAATTGCT
358105 TTAATTTTATTATTTG
65 TTAATTTTATTATTTG
*
358121 TTAATTTTATTATTACATTTTAATTAATTGATTTAAATATTGTTTCTATGGCTAATTAATTGCTT
1 TTAATATTATTATTACATTTTAATTAATTGATTTAAATATTGTTTCTATGGCTAATTAATTGCTT
358186 TAATTTTATTATTTG
66 TAATTTTATTATTTG
358201 ACAATTATTA
Statistics
Matches: 78, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
80 77 0.99
81 1 0.01
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (80 bp):
TTAATATTATTATTACATTTTAATTAATTGATTTAAATATTGTTTCTATGGCTAATTAATTGCTT
TAATTTTATTATTTG
Found at i:358145 original size:19 final size:16
Alignment explanation
Indices: 358104--358134 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
358094 AATTAATTGC
358104 TTTAATTTTATTATTT
1 TTTAATTTTATTATTT
*
358120 GTTAATTTTATTATT
1 TTTAATTTTATTATT
358135 ACATTTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTAATTTTATTATTT
Found at i:358318 original size:14 final size:16
Alignment explanation
Indices: 358282--358318 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
358272 TGTTATATTT
358282 TTTATTTTTTAAGTAA
1 TTTATTTTTTAAGTAA
*
358298 TTAATTTTTT-A-TAA
1 TTTATTTTTTAAGTAA
358312 TTTATTT
1 TTTATTT
358319 GTTTGATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
14 9 0.47
15 1 0.05
16 9 0.47
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTATTTTTTAAGTAA
Found at i:366850 original size:20 final size:21
Alignment explanation
Indices: 366820--366879 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 21
366810 CATTCTGGAG
*
366820 GAAATTGTATCGATACATTTT
1 GAAATTGTATCGATACATTTA
* * *
366841 TAAA-TGTATCGACACA-TAA
1 GAAATTGTATCGATACATTTA
366860 GAAATTGTATCGATACATTT
1 GAAATTGTATCGATACATTT
366880 CTCATTATAT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 4 0.13
20 22 0.73
21 4 0.13
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (21 bp):
GAAATTGTATCGATACATTTA
Found at i:369452 original size:74 final size:75
Alignment explanation
Indices: 369330--369468 Score: 210
Period size: 74 Copynumber: 1.9 Consensus size: 75
369320 TCTTTCGAGA
**
369330 GGATACTCCAACCTCTTTTTTTTAAAAAAAGTACTAATATTCAAATCTTATTTTGCCTAATTTAT
1 GGATACTCCAACCTCTTTTTTAAAAAAAAAGTACTAATATTCAAATCTTATTTTGCCTAATTTAT
369395 TGTTCATCCG
66 TGTTCATCCG
* * *
369405 GGATACTTCAACCT-TTTTTTAAAAAAAAATTA-TCAATATTCTAATCTTATTTTGCCTAATTTA
1 GGATACTCCAACCTCTTTTTTAAAAAAAAAGTACT-AATATTCAAATCTTATTTTGCCTAATTTA
369468 T
65 T
369469 CATTAATTAG
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
73 1 0.02
74 44 0.76
75 13 0.22
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (75 bp):
GGATACTCCAACCTCTTTTTTAAAAAAAAAGTACTAATATTCAAATCTTATTTTGCCTAATTTAT
TGTTCATCCG
Found at i:369485 original size:74 final size:75
Alignment explanation
Indices: 369332--369493 Score: 193
Period size: 74 Copynumber: 2.2 Consensus size: 75
369322 TTTCGAGAGG
** **
369332 ATACTCCAACCTCTTTTTTTTAAAAAAAGTACTAATATTCAAATCTTATTTTGCCTAATTTATTG
1 ATACTCCAACCTCTTTTTTAAAAAAAAAGTACTAATATTCAAATCTTATTTTGCCTAATTTATCA
* * *
369397 TTCATCCGGG
66 TTAATCAGGA
* * *
369407 ATACTTCAACCT-TTTTTTAAAAAAAAATTA-TCAATATTCTAATCTTATTTTGCCTAATTTATC
1 ATACTCCAACCTCTTTTTTAAAAAAAAAGTACT-AATATTCAAATCTTATTTTGCCTAATTTATC
*
369470 ATTAATTAGGA
65 ATTAATCAGGA
*
369481 ATACTCTAACCTC
1 ATACTCCAACCTC
369494 ATTCTTCTGA
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
73 1 0.01
74 60 0.83
75 11 0.15
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.43
Consensus pattern (75 bp):
ATACTCCAACCTCTTTTTTAAAAAAAAAGTACTAATATTCAAATCTTATTTTGCCTAATTTATCA
TTAATCAGGA
Found at i:372983 original size:23 final size:23
Alignment explanation
Indices: 372956--372999 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
372946 GTATTTAACC
* *
372956 TTGGGTTATAATTTTTTAAGAAT
1 TTGGGGTATAATTTTTGAAGAAT
372979 TTGGGGTATAATTTTTGAAGA
1 TTGGGGTATAATTTTTGAAGA
373000 GATTGAGAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.48
Consensus pattern (23 bp):
TTGGGGTATAATTTTTGAAGAAT
Found at i:374147 original size:3 final size:3
Alignment explanation
Indices: 374139--374200 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
374129 AACCATCAAA
* *
374139 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT AAT GAT GAT AAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
374187 GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GA
374201 AGTTGACTCA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.37, C:0.00, G:0.31, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:374343 original size:20 final size:20
Alignment explanation
Indices: 374320--374361 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
374310 AAAAGGACAA
374320 AGATCAAATTATATGCTATG
1 AGATCAAATTATATGCTATG
374340 AGATCAAATTATATGCTATG
1 AGATCAAATTATATGCTATG
374360 AG
1 AG
374362 TGTAAGAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (20 bp):
AGATCAAATTATATGCTATG
Found at i:380675 original size:34 final size:35
Alignment explanation
Indices: 380637--380703 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
380627 AAACAAGATC
*
380637 AAGGGCGAGAGATATTTTGA-AAATAAATTTGTAA
1 AAGGGCGAGAGATATTTTGAGAAATAAACTTGTAA
*
380671 AAGGGGGAGAGATATTTTGAGAAATAAACTTGT
1 AAGGGCGAGAGATATTTTGAGAAATAAACTTGT
380704 TTTATAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 19 0.63
35 11 0.37
ACGTcount: A:0.42, C:0.03, G:0.27, T:0.28
Consensus pattern (35 bp):
AAGGGCGAGAGATATTTTGAGAAATAAACTTGTAA
Found at i:380735 original size:13 final size:13
Alignment explanation
Indices: 380717--380743 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
380707 ATAAAGGGGG
380717 AGATTATTTTTGA
1 AGATTATTTTTGA
380730 AGATTATTTTTGA
1 AGATTATTTTTGA
380743 A
1 A
380744 ACAAAAAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (13 bp):
AGATTATTTTTGA
Found at i:386920 original size:19 final size:19
Alignment explanation
Indices: 386896--386932 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
386886 GTGTTTGAAA
386896 AAAAAAAAAAAAAAAATTG
1 AAAAAAAAAAAAAAAATTG
386915 AAAAAAAAAAAAAAAATT
1 AAAAAAAAAAAAAAAATT
386933 AAATGTATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAATTG
Found at i:386958 original size:21 final size:21
Alignment explanation
Indices: 386934--386990 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
386924 AAAAAAATTA
386934 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
386955 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
386976 AATGTATCGATACAT
1 AATGTATCGATACAT
386991 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:387070 original size:19 final size:19
Alignment explanation
Indices: 387046--387113 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
387036 AATTCAACAA
387046 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
387065 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
387080 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
387097 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
387114 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:387085 original size:13 final size:13
Alignment explanation
Indices: 387067--387091 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
387057 ACATAAGTTT
387067 TGTATCGATACAA
1 TGTATCGATACAA
387080 TGTATCGATACA
1 TGTATCGATACA
387092 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:387089 original size:32 final size:32
Alignment explanation
Indices: 387048--387110 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
387038 TTCAACAATT
*
387048 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
387080 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
387111 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:387171 original size:13 final size:13
Alignment explanation
Indices: 387153--387178 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
387143 CATTTTTCTG
387153 TGTATCGATACAT
1 TGTATCGATACAT
387166 TGTATCGATACAT
1 TGTATCGATACAT
387179 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:387175 original size:33 final size:33
Alignment explanation
Indices: 387133--387199 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
387123 GCCAAGGAAA
***
387133 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
387166 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
387199 T
1 T
387200 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:389718 original size:28 final size:27
Alignment explanation
Indices: 389651--389723 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
389641 CTTCACAATC
* *
389651 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
389678 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
389706 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
389724 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:389768 original size:51 final size:51
Alignment explanation
Indices: 389706--389877 Score: 191
Period size: 51 Copynumber: 3.3 Consensus size: 51
389696 TTATTTCTGA
* * *
389706 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
389757 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-AT-AATC
** * *
389811 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
389863 GAGGATACTCCAACC
1 GGGGATACTCCAACC
389878 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 1 0.01
54 31 0.32
55 11 0.11
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:389896 original size:28 final size:28
Alignment explanation
Indices: 389860--389941 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
389850 ATTTTTCACA
*
389860 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
389888 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
389916 --CGAGGGAACACTCCAATCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
389942 ATCTCCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 40 0.89
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.28
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:395509 original size:80 final size:82
Alignment explanation
Indices: 395415--395570 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 82
395405 CATACCCCGA
* * * * * *
395415 TGAAAAATTTGATATTTTGGAGATAAAA-TCGAGGTTGGAGTATCCCCTAAAAAATAATAAGGTT
1 TGAAAAATTCGATATTTCGAAAATAAAACT-GAGGTTAGAGTATCCCCTAAAAAATAACAAGGTT
395479 GGAGTA-TCCTCAATGGT
65 GGAGTATTCCTCAATGGT
* * * **
395496 TGAAAAA-TCGATATTTCGAAAATAAAACTGGGGTTAGAGTATCCCCTTAGAAATAACGGGGTTG
1 TGAAAAATTCGATATTTCGAAAATAAAACTGAGGTTAGAGTATCCCCTAAAAAATAACAAGGTTG
395560 GAGTATTCCTC
66 GAGTATTCCTC
395571 GAGATAAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
80 49 0.79
81 13 0.21
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (82 bp):
TGAAAAATTCGATATTTCGAAAATAAAACTGAGGTTAGAGTATCCCCTAAAAAATAACAAGGTTG
GAGTATTCCTCAATGGT
Found at i:395748 original size:79 final size:78
Alignment explanation
Indices: 395604--395828 Score: 206
Period size: 78 Copynumber: 2.9 Consensus size: 78
395594 TGAAAGTGAA
* * * **
395604 AACGGGGTTTGAGTATCCCCGATGGTGGGAATCGATATTTTAGAAATAAAACTGGGATTAGAGTA
1 AACGGGCTTGGAGTATCCCCAATGGTGAAAATCGATATTTTAGAAATAAAACTGGGATTAGAGTA
*
395669 TCCCCTCGAAAAT
66 TCCCATCGAAAAT
*
395682 AACGGGCTTGGAGTATCCCCAATGGTGAAAAATC-AGTATTTTAGAAATAAAA-TCGAGG-TTGG
1 AACGGGCTTGGAGTATCCCCAATGGTG-AAAATCGA-TATTTTAGAAATAAAACT-G-GGATTAG
*
395744 AGTATTCCATCGAAAAT
62 AGTATCCCATCGAAAAT
* ** ** * * * * * *
395761 AACGGGGTTAAAGTAT-CCTGATGGCGAAAAATTGATGTTTTGGAAATAAAACCGGGGTTAGAGT
1 AACGGGCTTGGAGTATCCCCAATGGTG-AAAATCGATATTTTAGAAATAAAACTGGGATTAGAGT
395825 ATCC
65 ATCC
395829 TCGAGATTAA
Statistics
Matches: 120, Mismatches: 20, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
77 2 0.02
78 63 0.52
79 53 0.44
80 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (78 bp):
AACGGGCTTGGAGTATCCCCAATGGTGAAAATCGATATTTTAGAAATAAAACTGGGATTAGAGTA
TCCCATCGAAAAT
Found at i:396415 original size:152 final size:152
Alignment explanation
Indices: 396139--396420 Score: 528
Period size: 152 Copynumber: 1.9 Consensus size: 152
396129 ATGTAGAATA
*
396139 AATCCTTGAACTCGGGTGTATGGCACTGTCAGTAGAACATATGAAAAAAATGGTATATTGAACTT
1 AATCCTTGAACTCAGGTGTATGGCACTGTCAGTAGAACATATGAAAAAAATGGTATATTGAACTT
396204 TGAAAAATCACCTCAGACTCATTTAGTATTGAAAAGTCATAAATAATACCTTTAAGAAAAGAGAA
66 TGAAAAATCACCTCAGACTCATTTAGTATTGAAAAGTCATAAATAATACCTTTAAGAAAAGAGAA
396269 AAAAGGCACTGTCATAAATGAT
131 AAAAGGCACTGTCATAAATGAT
*
396291 AATCCTTGAACTCAGGTGTATGGCACTGTCAGTAGAACATATGAGAAAAATGGTATATTGAACTT
1 AATCCTTGAACTCAGGTGTATGGCACTGTCAGTAGAACATATGAAAAAAATGGTATATTGAACTT
* *
396356 TGAAAAATCACTTCAGACTCATTTAGTATTGAAAAGTCATAAATTATACCTTTAAGAAAAGAGAA
66 TGAAAAATCACCTCAGACTCATTTAGTATTGAAAAGTCATAAATAATACCTTTAAGAAAAGAGAA
396421 TTTCATGAAA
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
152 126 1.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.28
Consensus pattern (152 bp):
AATCCTTGAACTCAGGTGTATGGCACTGTCAGTAGAACATATGAAAAAAATGGTATATTGAACTT
TGAAAAATCACCTCAGACTCATTTAGTATTGAAAAGTCATAAATAATACCTTTAAGAAAAGAGAA
AAAAGGCACTGTCATAAATGAT
Found at i:398386 original size:51 final size:51
Alignment explanation
Indices: 398312--398447 Score: 191
Period size: 51 Copynumber: 2.7 Consensus size: 51
398302 AAAAGGCCTT
* * *
398312 AATGTATCGATATATTGAGAAATGTATCGATACATCTAGGTTAAAACCCAA
1 AATGTATCGATACAATGAAAAATGTATCGATACATCTAGGTTAAAACCCAA
* * *
398363 AATGTATCGATACAATGAAAAATGTACCGATACATCTAGGTTAAAATCCAG
1 AATGTATCGATACAATGAAAAATGTATCGATACATCTAGGTTAAAACCCAA
* * *
398414 AATATATCTATACAATGAAAAAAGTATCGATACA
1 AATGTATCGATACAATGAAAAATGTATCGATACA
398448 AACAATAAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 75 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (51 bp):
AATGTATCGATACAATGAAAAATGTATCGATACATCTAGGTTAAAACCCAA
Found at i:399133 original size:19 final size:16
Alignment explanation
Indices: 399108--399178 Score: 70
Period size: 19 Copynumber: 4.0 Consensus size: 16
399098 GCGTCCTTCG
399108 AAAAAAATCAAATAAAAA
1 AAAAAAAT-AAA-AAAAA
399126 ATAAAAAATCACAAAAAAA
1 A-AAAAAAT-A-AAAAAAA
*
399145 GGAAAAAATAAAAAAATA
1 -AAAAAAATAAAAAAA-A
399163 AAAAAAATAAAAAAAA
1 AAAAAAATAAAAAAAA
399179 GAGAGAGAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
16 1 0.02
17 20 0.43
18 3 0.06
19 21 0.45
20 2 0.04
ACGTcount: A:0.83, C:0.04, G:0.03, T:0.10
Consensus pattern (16 bp):
AAAAAAATAAAAAAAA
Found at i:399158 original size:8 final size:8
Alignment explanation
Indices: 399117--399177 Score: 61
Period size: 8 Copynumber: 7.4 Consensus size: 8
399107 GAAAAAAATC
399117 AAAT-AAA
1 AAATAAAA
399124 AAATAAAA
1 AAATAAAA
*
399132 AATCACAAAA
1 AA--ATAAAA
**
399142 AAAGGAAA
1 AAATAAAA
399150 AAATAAAA
1 AAATAAAA
399158 AAATAAAAA
1 AAAT-AAAA
399167 AAATAAAA
1 AAATAAAA
399175 AAA
1 AAA
399178 AGAGAGAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
7 4 0.09
8 26 0.58
9 8 0.18
10 7 0.16
ACGTcount: A:0.84, C:0.03, G:0.03, T:0.10
Consensus pattern (8 bp):
AAATAAAA
Found at i:399159 original size:9 final size:9
Alignment explanation
Indices: 399108--399178 Score: 58
Period size: 8 Copynumber: 7.8 Consensus size: 9
399098 GCGTCCTTCG
399108 AAAAAAATCA
1 AAAAAAAT-A
399118 AATAAAAA-A
1 AA-AAAAATA
*
399127 TAAAAAATCA
1 AAAAAAAT-A
*
399137 CAAAAAAA-G
1 -AAAAAAATA
*
399146 GAAAAAAT-
1 AAAAAAATA
399154 AAAAAAATA
1 AAAAAAATA
399163 AAAAAAATA
1 AAAAAAATA
399172 AAAAAAA
1 AAAAAAA
399179 GAGAGAGAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
8 18 0.36
9 18 0.36
10 3 0.06
11 11 0.22
ACGTcount: A:0.83, C:0.04, G:0.03, T:0.10
Consensus pattern (9 bp):
AAAAAAATA
Found at i:400383 original size:13 final size:13
Alignment explanation
Indices: 400365--400406 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
400355 AGAGGTTATC
400365 GTCAAGAACTTTT
1 GTCAAGAACTTTT
*
400378 GTCAAGAACGTTT
1 GTCAAGAACTTTT
*
400391 GTCAA-AAATTTT
1 GTCAAGAACTTTT
400403 GTCA
1 GTCA
400407 CGAAATTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 9 0.35
13 17 0.65
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (13 bp):
GTCAAGAACTTTT
Found at i:400405 original size:12 final size:13
Alignment explanation
Indices: 400365--400413 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
400355 AGAGGTTATC
*
400365 GTCAAGAACTTTT
1 GTCAAGAAATTTT
**
400378 GTCAAGAACGTTT
1 GTCAAGAAATTTT
400391 GTCAA-AAATTTT
1 GTCAAGAAATTTT
*
400403 GTCACGAAATT
1 GTCAAGAAATT
400414 GTTATCAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
12 9 0.29
13 22 0.71
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (13 bp):
GTCAAGAAATTTT
Found at i:400859 original size:32 final size:32
Alignment explanation
Indices: 400634--401026 Score: 292
Period size: 32 Copynumber: 12.0 Consensus size: 32
400624 TTAGTGGAGA
* * * *
400634 AACCTTTTTCAAAAGCTCACATAGGTTGGTGGC
1 AACCTTCTTC-AAAGCCCACACAAGTTGGTGGC
* *
400667 AACCTTCTTTAAAAGCCCATACAAGTTGGTGGC
1 AACCTTC-TTCAAAGCCCACACAAGTTGGTGGC
***
400700 AACCTTTCCTTCCAAAAG-CCACA-AA-TAAATGGC
1 AACC-TT-CTT-C-AAAGCCCACACAAGTTGGTGGC
*** *
400733 ATTTTTTTCCTTCAAAGGCCCACACAAGTTGGTAGC
1 A--ACCTT-CTTCAAA-GCCCACACAAGTTGGTGGC
* * * ****
400769 AACCTTTTTCAAAGCTCATACAAACCAGTGGC
1 AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
* **
400801 AACCTTCTTCAAAAGCCAACTTAAGTTGGTGGC
1 AACCTTCTTC-AAAGCCCACACAAGTTGGTGGC
400834 AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
1 AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
* *
400866 AACCATC-TCAAAAGCCCACACAAGCTGGTGGC
1 AACCTTCTTC-AAAGCCCACACAAGTTGGTGGC
* *
400898 AAACTTCTTCAAAGCCCATACAAGTTGGTGGC
1 AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
* * * * * * * *
400930 AACCCTC-TCAAAAACCTATATAAGCTGATAGC
1 AACCTTCTTC-AAAGCCCACACAAGTTGGTGGC
400962 AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
1 AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
* * *
400994 AACCCTCTTAAAAGCCAACACAAGTTGGTGGC
1 AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
401026 A
1 A
401027 TCTCCTTCAA
Statistics
Matches: 277, Mismatches: 67, Indels: 33
0.73 0.18 0.09
Matches are distributed among these distances:
31 4 0.01
32 167 0.60
33 69 0.25
34 21 0.08
35 7 0.03
36 9 0.03
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (32 bp):
AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
Found at i:400905 original size:64 final size:64
Alignment explanation
Indices: 400744--401026 Score: 323
Period size: 64 Copynumber: 4.4 Consensus size: 64
400734 TTTTTTTCCT
* * * * * * **** *
400744 TCAAAGGCCCACACAAGTTGGTAGCAACCTTTTTCAAAGCTCATACAAACCAGTGGCAACCTTC
1 TCAAAAGCCAACACAAGTTGGTGGCAACCTTCTTCAAAGCCCACACAAGTTGGTGGCAACCCTC
** *
400808 TTCAAAAGCCAACTTAAGTTGGTGGCAACCTTCTTCAAAGCCCACACAAGTTGGTGGCAACCATC
1 -TCAAAAGCCAACACAAGTTGGTGGCAACCTTCTTCAAAGCCCACACAAGTTGGTGGCAACCCTC
* * * *
400873 TCAAAAGCCCACACAAGCTGGTGGCAAACTTCTTCAAAGCCCATACAAGTTGGTGGCAACCCTC
1 TCAAAAGCCAACACAAGTTGGTGGCAACCTTCTTCAAAGCCCACACAAGTTGGTGGCAACCCTC
* * * * * * *
400937 TCAAAAACCTATATAAGCTGATAGCAACCTTCTTCAAAGCCCACACAAGTTGGTGGCAACCCTC
1 TCAAAAGCCAACACAAGTTGGTGGCAACCTTCTTCAAAGCCCACACAAGTTGGTGGCAACCCTC
*
401001 TTAAAAGCCAACACAAGTTGGTGGCA
1 TCAAAAGCCAACACAAGTTGGTGGCA
401027 TCTCCTTCAA
Statistics
Matches: 182, Mismatches: 36, Indels: 1
0.83 0.16 0.00
Matches are distributed among these distances:
64 131 0.72
65 51 0.28
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (64 bp):
TCAAAAGCCAACACAAGTTGGTGGCAACCTTCTTCAAAGCCCACACAAGTTGGTGGCAACCCTC
Found at i:401287 original size:108 final size:105
Alignment explanation
Indices: 401170--401374 Score: 245
Period size: 108 Copynumber: 1.9 Consensus size: 105
401160 CTAATTTTGA
* * *
401170 ATCAGCACATTAGTACTTT-TATGATCTTTAAGCCCAATATCGTTGGTC-GTGAATCAGCATA-T
1 ATCAACACATTAGCACTTTCT-TCATCTTTAAGCCCAATATCGTTGG-CAGTGAATCAGCATATT
*
401232 TGGCATTTTTTTTATCATCTTCAAAGTCTAATGTCGCTAGCCCTAT
64 TGGCA---TTCTTATCATCTT-AAAGTCTAATGTCGCTAGCCCTAT
* * * * *
401278 ATCAACACATTAGCACTTTCTTCATCTTTAAGTCCAATGTTGTTGGCATTGAATTAGCATATTTG
1 ATCAACACATTAGCACTTTCTTCATCTTTAAGCCCAATATCGTTGGCAGTGAATCAGCATATTTG
*
401343 GCATTCTTATCATCTTTAAGTCTAATGTCGCT
66 GCATTCTTATCATCTTAAAGTCTAATGTCGCT
401375 GGGCTTGAAT
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
105 15 0.18
106 12 0.14
107 1 0.01
108 49 0.58
109 7 0.08
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (105 bp):
ATCAACACATTAGCACTTTCTTCATCTTTAAGCCCAATATCGTTGGCAGTGAATCAGCATATTTG
GCATTCTTATCATCTTAAAGTCTAATGTCGCTAGCCCTAT
Found at i:401356 original size:53 final size:52
Alignment explanation
Indices: 401299--401476 Score: 232
Period size: 53 Copynumber: 3.4 Consensus size: 52
401289 AGCACTTTCT
*
401299 TCATCTTTAAGTCCAATGTTGTTGGCATTGAATTAGCATATTTGGCATTCTTA
1 TCATCTTTAAGTCCAATGTCGTTGGC-TTGAATTAGCATATTTGGCATTCTTA
* * * *
401352 TCATCTTTAAGTCTAATGTCGCTGGGCTTGAATTAGCACATTTGGCCTTCTTA
1 TCATCTTTAAGTCCAATGTCG-TTGGCTTGAATTAGCATATTTGGCATTCTTA
* * *
401405 TCATCTTTAAGTCCAATGGCGTTGGCCTTGAA-TAACATTTTTGGCATTCTTA
1 TCATCTTTAAGTCCAATGTCGTTGG-CTTGAATTAGCATATTTGGCATTCTTA
* *
401457 TCATCTTTGAGTCCGATGTC
1 TCATCTTTAAGTCCAATGTC
401477 TCTGGCCTTA
Statistics
Matches: 108, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
52 36 0.33
53 68 0.63
54 4 0.04
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (52 bp):
TCATCTTTAAGTCCAATGTCGTTGGCTTGAATTAGCATATTTGGCATTCTTA
Found at i:401462 original size:105 final size:106
Alignment explanation
Indices: 401299--401498 Score: 285
Period size: 105 Copynumber: 1.9 Consensus size: 106
401289 AGCACTTTCT
** *
401299 TCATCTTTAAGTCCAATGTTGTTGGCATTGAATTAGCATATTTGGCATTCTTATCATCTTTAAGT
1 TCATCTTTAAGTCCAATGGCGTTGGCATTGAATTAACATATTTGGCATTCTTATCATCTTTAAGT
* * * *
401364 CTAATGTCGCTGGGCTTGAATTAGCACATTTGGCCTTCTTA
66 CCAATGTCGCTGGCCTTAAACTAGCACATTTGGCCTTCTTA
* * *
401405 TCATCTTTAAGTCCAATGGCGTTGGCCTTGAA-TAACATTTTTGGCATTCTTATCATCTTTGAGT
1 TCATCTTTAAGTCCAATGGCGTTGGCATTGAATTAACATATTTGGCATTCTTATCATCTTTAAGT
* *
401469 CCGATGTCTCTGGCCTTAAACTAGCACATT
66 CCAATGTCGCTGGCCTTAAACTAGCACATT
401499 AGCACCTTTA
Statistics
Matches: 82, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
105 53 0.65
106 29 0.35
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (106 bp):
TCATCTTTAAGTCCAATGGCGTTGGCATTGAATTAACATATTTGGCATTCTTATCATCTTTAAGT
CCAATGTCGCTGGCCTTAAACTAGCACATTTGGCCTTCTTA
Found at i:402300 original size:20 final size:21
Alignment explanation
Indices: 402250--402300 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
402240 ATTCTGGAAG
**
402250 GAAATTGTATCGATACACTTT
1 GAAATTGTATCGATACACTAA
* *
402271 TAAA-TATATCGATACA-TAA
1 GAAATTGTATCGATACACTAA
402290 GAAATTGTATC
1 GAAATTGTATC
402301 AATAGATTTC
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
19 4 0.17
20 16 0.70
21 3 0.13
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (21 bp):
GAAATTGTATCGATACACTAA
Found at i:402373 original size:20 final size:20
Alignment explanation
Indices: 402348--402398 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
402338 GACAGAAATG
402348 TATCGATACATTTTTCAATA
1 TATCGATACATTTTTCAATA
* *
402368 TATCGATATATTTTTCAATG
1 TATCGATACATTTTTCAATA
402388 TATCGATACAT
1 TATCGATACAT
402399 CCAGTTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (20 bp):
TATCGATACATTTTTCAATA
Found at i:403267 original size:20 final size:20
Alignment explanation
Indices: 403244--403281 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
403234 ACACCCAGAT
403244 GTATCGATACAAATTGCTAA
1 GTATCGATACAAATTGCTAA
403264 GTATCGATACAAATTGCT
1 GTATCGATACAAATTGCT
403282 TTGCATCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (20 bp):
GTATCGATACAAATTGCTAA
Found at i:403883 original size:35 final size:34
Alignment explanation
Indices: 403832--403897 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 34
403822 GAAGTAATTG
*
403832 AGAGGTTCTATATTAGCCTTTGAAAAAGATAGGGA
1 AGAGGTTCTATATTAGCCTATG-AAAAGATAGGGA
*
403867 AGAGGTTCTATCTTAGCCTATGAAAAGATAG
1 AGAGGTTCTATATTAGCCTATGAAAAGATAG
403898 AGTGGTAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 9 0.31
35 20 0.69
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (34 bp):
AGAGGTTCTATATTAGCCTATGAAAAGATAGGGA
Found at i:408313 original size:33 final size:33
Alignment explanation
Indices: 408276--408342 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
408266 AGTAGCTTAA
408276 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
408309 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
408342 A
1 A
408343 AATCATCGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:408316 original size:13 final size:13
Alignment explanation
Indices: 408298--408322 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
408288 CAAAAAAATA
408298 TGTATCGATACAT
1 TGTATCGATACAT
408311 TGTATCGATACA
1 TGTATCGATACA
408323 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:410491 original size:31 final size:31
Alignment explanation
Indices: 410435--410494 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
410425 CTTTGTCTAG
*
410435 TTGGAAATGATGGCGCTTTAAATTTTCCACT
1 TTGGAAATGATGGCGCTTCAAATTTTCCACT
* **
410466 TTGGAAATTATGGCGCTTCGGATTTTCCA
1 TTGGAAATGATGGCGCTTCAAATTTTCCA
410495 TTTTCTCTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (31 bp):
TTGGAAATGATGGCGCTTCAAATTTTCCACT
Found at i:413679 original size:2 final size:2
Alignment explanation
Indices: 413672--413715 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
413662 CATAATTTGC
413672 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
413714 TA
1 TA
413716 GAAGAAATAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:415505 original size:12 final size:12
Alignment explanation
Indices: 415460--415534 Score: 66
Period size: 12 Copynumber: 6.3 Consensus size: 12
415450 TGTAAATTTT
*
415460 TTTCTTTTTTTC
1 TTTCTTTCTTTC
*
415472 ATT-TTTCTTT-
1 TTTCTTTCTTTC
415482 TTT-TTCTCCTTTC
1 TTTCTT-T-CTTTC
415495 TTTCTTTCTTTC
1 TTTCTTTCTTTC
*
415507 TTTTTTTCTTTC
1 TTTCTTTCTTTC
* *
415519 TTTTTTTCCTTC
1 TTTCTTTCTTTC
415531 TTTC
1 TTTC
415535 CCAGCCAAAC
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
10 4 0.08
11 7 0.13
12 36 0.68
13 4 0.08
14 2 0.04
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTCTTTCTTTC
Found at i:415535 original size:8 final size:8
Alignment explanation
Indices: 415460--415534 Score: 66
Period size: 8 Copynumber: 9.5 Consensus size: 8
415450 TGTAAATTTT
*
415460 TTTCTTTT
1 TTTCTTTC
*
415468 TTTCATT-
1 TTTCTTTC
415475 TTTCTTT-
1 TTTCTTTC
415482 TTT-TTCTCC
1 TTTCTT-T-C
415491 TTTCTTTC
1 TTTCTTTC
415499 TTTCTTTC
1 TTTCTTTC
*
415507 TTTTTTTC
1 TTTCTTTC
*
415515 TTTCTTTT
1 TTTCTTTC
*
415523 TTTCCTTC
1 TTTCTTTC
415531 TTTC
1 TTTC
415535 CCAGCCAAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
6 2 0.04
7 10 0.18
8 38 0.68
9 4 0.07
10 2 0.04
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTCTTTC
Found at i:418436 original size:2 final size:2
Alignment explanation
Indices: 418429--418462 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
418419 CGGTTATTTA
418429 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
418463 GTATTCAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:419404 original size:139 final size:139
Alignment explanation
Indices: 419150--419407 Score: 351
Period size: 139 Copynumber: 1.8 Consensus size: 139
419140 ATCGATCTAC
* *
419150 TTTTGCTTTAAACTCAATGTACAGATGACTACGTTTTCATATGTATATATTTTTTGCACCCAGAT
1 TTTTGCTTTAAACTCAATGAACAGA-GACTACGTTTTCATATGTATATATTTGTTGCACCCAGAT
* * *
419215 TAAGCCATGTATGTGTATAAATAACTATATTTTAATCATATATATAGTTACACTATCTTATTGTG
65 TAAGACATGTATGAGTACAAATAACTATATTTTAATCATATATATAGTTACACTATCTTATTGTG
419280 TATATATATT
130 TATATATATT
* *
419290 TTTTGCTTTAAACTCGATGAACA-AGCAACTATGTTTTCATATGTATATA-TTGTTGCACCCA-A
1 TTTTGCTTTAAACTCAATGAACAGAG--ACTACGTTTTCATATGTATATATTTGTTGCACCCAGA
* * * * *
419352 CTTCAGACATGTATGAGTACAAATAACTATATTTTGATTATGTATATGGTTACACT
64 -TTAAGACATGTATGAGTACAAATAACTATATTTTAATCATATATATAGTTACACT
419408 GTCAACCATT
Statistics
Matches: 103, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
138 2 0.02
139 59 0.57
140 42 0.41
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (139 bp):
TTTTGCTTTAAACTCAATGAACAGAGACTACGTTTTCATATGTATATATTTGTTGCACCCAGATT
AAGACATGTATGAGTACAAATAACTATATTTTAATCATATATATAGTTACACTATCTTATTGTGT
ATATATATT
Found at i:419844 original size:22 final size:23
Alignment explanation
Indices: 419812--419856 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
419802 TTCTTTATAT
419812 TATTAAAATATTTTTAT-ATTAA
1 TATTAAAATATTTTTATAATTAA
*
419834 TATTAATATATTTTTATAATTAA
1 TATTAAAATATTTTTATAATTAA
419857 ATTTAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTAAAATATTTTTATAATTAA
Found at i:420944 original size:26 final size:30
Alignment explanation
Indices: 420880--420948 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 30
420870 ATTTCTTGAA
*
420880 TATTATTAAACATAAATATTAATACATTAT
1 TATTATTTAACATAAATATTAATACATTAT
*
420910 TAATA-TTAACA-AAA-A-TAATACATT-T
1 TATTATTTAACATAAATATTAATACATTAT
420935 TATTATTTAA-ATAA
1 TATTATTTAACATAA
420949 TAAATATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
25 6 0.18
26 15 0.44
27 1 0.03
28 3 0.09
29 5 0.15
30 4 0.12
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (30 bp):
TATTATTTAACATAAATATTAATACATTAT
Found at i:424240 original size:26 final size:26
Alignment explanation
Indices: 424211--424260 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
424201 CATGTTTAGC
424211 ATGCAGTATGCTACGTTACAAACCGT
1 ATGCAGTATGCTACGTTACAAACCGT
424237 ATGCAGTATGCTACGTTACAAACC
1 ATGCAGTATGCTACGTTACAAACC
424261 ATTTTAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (26 bp):
ATGCAGTATGCTACGTTACAAACCGT
Found at i:425743 original size:18 final size:18
Alignment explanation
Indices: 425720--425756 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
425710 TCATGCCCTC
425720 AGCCTGTTGTAATTTTAT
1 AGCCTGTTGTAATTTTAT
425738 AGCCTGTTGTAATTTTAT
1 AGCCTGTTGTAATTTTAT
425756 A
1 A
425757 CTCCATGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.49
Consensus pattern (18 bp):
AGCCTGTTGTAATTTTAT
Found at i:427733 original size:22 final size:23
Alignment explanation
Indices: 427701--427746 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
427691 CATTTCCAAT
*
427701 ATTTACTTTTG-ATGTTTTAAAAG
1 ATTTACTTTTGTA-GCTTTAAAAG
427724 ATTTA-TTTTGTAGCTTTAAAAG
1 ATTTACTTTTGTAGCTTTAAAAG
427746 A
1 A
427747 CTCATTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (23 bp):
ATTTACTTTTGTAGCTTTAAAAG
Found at i:429861 original size:22 final size:22
Alignment explanation
Indices: 429820--429860 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
429810 TTTACTTAGC
429820 TTTTATTTGTTACAATATAATA
1 TTTTATTTGTTACAATATAATA
429842 TTTTATTT-TTA-AAT-TAATA
1 TTTTATTTGTTACAATATAATA
429861 AAAACTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 3 0.16
21 3 0.16
22 8 0.42
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTATTTGTTACAATATAATA
Found at i:432518 original size:16 final size:16
Alignment explanation
Indices: 432499--432545 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
432489 AAATATTATA
432499 AATTTATATAAATTTT
1 AATTTATATAAATTTT
*
432515 AATTTAT-TAATAATTT
1 AATTTATATAA-ATTTT
432531 -ATATTATATAAATTT
1 AAT-TTATATAAATTT
432546 AATATATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 5 0.19
16 18 0.69
17 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTTATATAAATTTT
Found at i:432520 original size:32 final size:31
Alignment explanation
Indices: 432471--432545 Score: 73
Period size: 32 Copynumber: 2.4 Consensus size: 31
432461 ATTATTTTTA
*
432471 TATATTAAATTATATTTA-AAATA-TTATAAATT
1 TATA-TAAATTTTATTTATAAATAATT-TAAA-T
* *
432503 TATATAAATTTTAATTTATTAATAATTTATAT
1 TATATAAATTTT-ATTTATAAATAATTTAAAT
432535 TATATAAATTT
1 TATATAAATTT
432546 AATATATTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
31 7 0.19
32 21 0.57
33 7 0.19
34 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TATATAAATTTTATTTATAAATAATTTAAAT
Found at i:432522 original size:27 final size:27
Alignment explanation
Indices: 432484--432566 Score: 78
Period size: 27 Copynumber: 2.9 Consensus size: 27
432474 ATTAAATTAT
*
432484 ATTTAAAATATT-ATAAATTTATATAA
1 ATTTAATATATTAATAAATTTATATAA
*
432510 ATTTTAATTTATTAATAATTTATATTATATAA
1 A-TTTAATATATTAATAA---AT-TTATATAA
* *
432542 ATTTAATATATTCATATATTTATAT
1 ATTTAATATATTAATAAATTTATAT
432567 TATTTTTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
26 1 0.02
27 15 0.33
28 6 0.13
31 15 0.33
32 9 0.20
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (27 bp):
ATTTAATATATTAATAAATTTATATAA
Done.